betweenes centrality fixed

Former-commit-id: c3e7bd3cf65e180f9153272087c802aad19e0061 [formerly e34d9a36054a15f0fe8bd3461c66f75fd333e1ee]
Former-commit-id: bd35491f003f79dc5b47609a542b3e2a636f02b5

tasks/betweenness_centrality.py

@@ -181,6 +181,7 @@ def betweenness_centrality(task_hook: TaskHook):
     g, seed_ids, drug_ids = read_graph_tool_graph(
         filename,
         seeds,
+        id_space,
         max_deg,
         include_indirect_drugs,
         include_non_approved_drugs,

tasks/keypathwayminer_task.py

@@ -213,7 +213,7 @@ def kpm_task(task_hook: TaskHook):
         if id_space == 'ensembl':
             node_map[node.uniprot_code] = [ensg.name for ensg in EnsemblGene.objects.filter(protein_id=node.id)]
 
-    flat_map = lambda f, xs: [y for ys in xs for y in f(ys)]
+    flat_map = lambda f, xs: (y for ys in xs for y in f(ys))
 
     network["nodes"] = flat_map(lambda uniprot: node_map[uniprot], network["nodes"])
     network["edges"] = list(map(

tasks/util/read_graph_tool_graph.py

@@ -92,8 +92,9 @@ def read_graph_tool_graph(file_path, seeds, id_space, max_deg, include_indirect_
 
     deleted_edges = []
 
-    if (
-            drug_ids and not include_indirect_drugs):  # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of any seeds
+    # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of
+    # any seeds
+    if drug_ids and not include_indirect_drugs:
         direct_drugs = set()
         for edge in g.edges():
             if g.vertex_properties["type"][edge.target()] == d_type and edge.source() in seed_ids: